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79 results for “positive interactions”
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
<p>Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by the environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. For this purpose, we generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high Arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more likely reflect interactive associations. Our results indicate that positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.</p>
Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats
<p><span>S</span><span>pecies</span><span> and their interactions are more dynamic over time and space</span> <span>in</span><span> fragmented habitats </span><span>than</span><span> in continuous habitats</span><span>.</span> <span>In fragmented habitats,</span><span> the</span> <span>low </span><span>nestedness</span> <span>of </span><span>mutualistic</span><span> networks may be related to the</span> <span>position</span><span> change</span> <span>of stable (high persistence over time/space) species and interactions in </span><span>the</span><span> network</span><span>s.</span><span> Previous studies</span> <span>have shown that </span><span>s</span><span>table species </span><span>and</span><span> interactions tend to </span><span>be in</span><span> the core position </span><span>of</span> <span>mutualistic</span><span> networks</span><span>. </span><span>H</span><span>owever</span><span>, </span><span>in fragmented habitats</span><span>, </span><span>it remains unknown whether </span><span>stable species or interactions still </span><span>tend to </span><span>be in</span><span> the core position.</span><span> </span><span>To address this gap,</span> <span>here</span><span> we evaluated </span><span>the correlation between the position of proximity to the network core and the temporal/spatial stability of </span><span>species and interactions</span><span>, </span><span>using</span> <span>the </span><span>observation of 42 plant-pollinator networks conducted in a fragmented island landscape over 3 years</span><span>.</span> <span>We showed that temporally/spatially </span><span>stable </span><span>species </span><span>and</span><span> interactions </span><span>deviated from the network core</span><span> to varying degrees</span><span>. Temporally stable plants</span><span> were</span> <span>most likely to deviate from the network core, followed by</span> <span>pollinators and</span> <span>interactions</span><span>, while only </span><span>spatially stable </span><span>pollinators</span><span> tend to </span><span>deviate from the network core</span><span>. </span><span>When unstable species (</span><span>present in few time/space points</span><span>, </span><span>typically specialists) and interactions occupy the network core,</span> <span>they cannot interact with most species in the network </span><span>as</span><span> generalists</span> <span>do</span><span>, </span><span>result</span><span>ing</span> <span>in</span> <span>the</span> <span>decrease of network nestedness. Therefore, from the perspective of</span><span> position and stability,</span><span> s</span><span>table species and interactions </span><span>deviate from the network core</span> <span>in</span> <span>fragmented habitats</span><span>, which </span><span>is an important reason for</span><span> the</span><span> decrease of</span><span> nestedness in </span><span>mutualistic</span><span> networks</span><span>.</span><span> </span><span>Our study</span><span> suggests that protecting</span> <span>plants that</span><span> occupy the core in large plant-pollinator networks is </span><span>essential for</span> <span>maintaining the network persistence in fragmented habitats.</span></p>
Figure 5. The distortion is barely noticeable if the faces are viewed in the reversed position-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>According to the feature-based processing theories of human faces the main elements,<br> noticed and remembered in a face, are the eyes, the nose and the mouth (Thompson, 1980; Anstis,<br> 2005a). If, however, we distort some of the elements of a face, these should influence perception,regardless of the position of the image – upright or reversed – from the observer viewpoint. Figure 5<br> presents the reversed image of the face on the left and the reversed distorted face on the right. The<br> distortion was achieved by rotating the eyes of the image in the vertical direction.<br> Figure</p>
CNN models and training, validation and test datasets for "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"
<p>Convolutional neural network (CNN) models and their respective training, validation and test datasets used in manuscript:</p> <p>Tuomo Hartonen, Teemu Kivioja and Jussi Taipale, "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"</p>
A Phase 1 Drug-Drug Interaction Study Between Brigatinib and the CYP3A Substrate, Midazolam, in Participants With ALK-Positive or ROS1-Positive Solid Tumors
ClinicalTrials.gov study NCT03420742. IPD Sharing: YES. Countries: 4. Publications: 1.
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
Open the record for dataset details and reuse information.
Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats
Open the record for dataset details and reuse information.
Positive and negative interspecific interactions between coexisting rice planthoppers neutralize the effects of elevated temperatures
Global warming is often predicted to increase damage to plants through direct effects on insect herbivores. However, the indirect impacts of rising temperatures on herbivores, mediated through interactions with their biotic environment, could dampen these effects. Using a series of reciprocal density experiments with gravid females and developing nymphs, we examined interspecific competition between two coexisting phloem feeders, Nilaparvata lugens (BPH) and Sogatella furcifera (WBPH), on rice at 25°C and 30°C. WBPH performed better (i.e., adults survived longer, nymphs developed faster and grew larger) at 25°C and BPH (i.e., nymphs developed faster) at 30°C. However, contrary to predictions, WBPH had a greater effect in reducing oviposition and nymph performance in BPH at 30°C. A decoupling of resource use by WBPH and its antagonistic effects on BPH at the higher temperature suggests that WBPH feeding induces host defenses that reduce BPH fitness (i.e., interference competition). Meanwhile, BPH facilitated WBPH oviposition at 30°C and facilitated WBPH nymph performance at 25 and 30°C. Greater facilitation of feeding in WBPH nymphs by BPH at high densities suggests that mechanical damage and host responses to damage increased the fitness of the heterospecific nymphs. Although BPH also facilitated egg-laying by WBPH, intra- and interspecific crowding countered this facilitation at both temperatures. Simulated life tables for planthoppers at 25 and 30°C depicted significantly lower offspring numbers on rice infested by WBPH alone and from mixed BPH-WBPH infestations than from infestations by BPH alone. Our results indicate how interference competition – mediated through host plant defenses - can increase ecosystem resilience to the warmer temperatures predicted under global climate change.
Positive species interactions strengthen in a high-CO2 ocean
<p>Negative interactions among species are a major force shaping natural communities and are predicted to strengthen as climate change intensifies. Similarly, positive interactions are anticipated to intensify, and could buffer the consequences of climate-driven disturbances. We used in situ experiments at volcanic CO2 vents within a temperate rocky reef to show that ocean acidification can drive community reorganization through indirect and direct positive pathways. A keystone species, the algal-farming damselfish Parma alboscapularis, enhanced primary productivity through its weeding of algae whose productivity was also boosted by elevated CO2. The accelerated primary productivity translated into increased densities of primary consumers (herbivorous invertebrates), which indirectly supported increased secondary consumers densities (predatory fish) (i.e. strengthening of bottom-up fuelling). However, this keystone species also reduced predatory fish densities through behavioural interference, releasing invertebrate prey from predation pressure and enabling a further boost in prey densities (i.e. weakening of top-down control). We uncover a novel mechanism where a keystone herbivore mediates bottom-up and top-down processes simultaneously to boost populations of a co-existing herbivore, resulting in altered food web interactions and predator populations under future ocean acidification.</p>
RecView: An interactive R application for locating recombination positions using pedigree data
<p><span>We present <em>RecView</em>, an interactive R application and </span><span>its homonymous R package</span><span>, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. </span><span>We demonstrate applicability of <em>RecView </em>using the genotype data from two offspring, as well as their grandparents and parents, of the great reed warbler (<em>Acrocephalus arundinaceus</em>).</span></p>
Datasets of positive and negative miRNA-target interactions from 4 species
<p>The datasets provided accompany the paper "Empowering Prediction of miRNA-mRNA Interactions in Species with Limited Training Data through Transfer Learning." These datasets encompass all positive and negative data relevant to the paper.</p> <p>The datasets were created in a prior paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04164-x) by Gilad Ben-Or.</p> <div> <p> </p> </div>
Metapopulation-level associations in positively interacting stream fishes
<p>Positive biotic interactions are recognized as important factors determining species distributions. Although effects of positive interactions have often been observed at local scales, much less is known about consequences at larger spatial scales. Here, we study nest associations of stream fishes - widespread reproductive facilitation between host (nest-builder) and beneficiary (nest associate) species in North America - as a model system to examine the role of positive interactions in determining the metapopulation-level relationship between host and beneficiary species. Using regional data of fish distribution in the Midwestern US, we found that watershed-level occupancy of host species (i.e., metapopulation occupancy) remarkably increased that of nest associates. Our results illustrated that the effects of positive biotic interactions at the metapopulation level were comparable or even stronger than environmental drivers, i.e., factors that have been studied most extensively in metapopulation studies. Further, our model supported the hypothesis that the metapopulation-level relationship between hosts and nest associates was mediated by a gradient of environmental conditions: strong associations occurred under stressful habitats. This study provides insightful evidence that positive biotic interactions have larger scale consequences for distributions of organisms than previously thought. Successful biodiversity conservation may need a broader framework that appreciates the role of positive biotic interactions at larger spatial scales.</p>
Positive interactions between corals and damselfish increase coral resistance to temperature stress
<p>By the century's end, many tropical seas will reach temperatures exceeding most coral species' thermal tolerance on an annual basis. The persistence of corals in these regions will therefore depend on their abilities to tolerate recurrent thermal stress. Although ecologists have long recognized that positive interspecific interactions can ameliorate environmental stress to expand the realized niche of plants and animals, coral bleaching studies have largely overlooked how interactions with community members outside of the coral holobiont shape the bleaching response. Here, we subjected a common coral, <em>Pocillopora</em> <em>grandis</em>, to 10 days of thermal stress in aquaria with- and without the damselfish <em>Dascyllus</em> <em>flavicaudus</em> (yellowtail dascyllus), which commonly shelter within these corals, to examine how interactions with damselfish impacted coral thermal tolerance. Corals often benefit from nutrients excreted by animals they interact with and prior to thermal stress, corals grown with damselfish showed improved photophysiology (F<sub>v</sub>/F<sub>m</sub>) and developed larger endosymbiont populations. When exposed to thermal stress, corals with fish performed as well as corals maintained at ambient temperatures without fish. In contrast, corals exposed to thermal stress without fish experienced photophysiological impairment, a more than 50% decline in endosymbiont density, and a 36% decrease in tissue protein content. By the end of the experiment, thermal stress caused average calcification rates to decrease by over 80% when damselfish were absent but increase nearly 25% when damselfish were present. Our study indicates that damselfish-derived nutrients can increase coral thermal tolerance and are consistent with the Stress Gradient Hypothesis, which predicts that positive interactions become increasingly important for structuring communities as environmental stress increases. Because warming of just a few degrees can exceed corals' temperature tolerance to trigger bleaching and mortality, positive interactions could play a critical role in maintaining some coral species in warming regions until climate change is aggressively addressed.</p>
Precise positioning of gamma ray interactions in multiplexed pixelated scintillators using artificial neural networks
<p>Data used to train multiclass and binary neural networks to analyse SiPM (Silicon Photomultiplier) signals in a multiplexed array of 16 detectors and detect the signal detector origin. Data acquired using an oscilloscope. Results compared with previous anger logic methods. </p> <p>Dataset used in the publication</p> <p>"Precise positioning of gamma ray interactions in multiplexed pixelated scintillators using artificial neural networks"</p> <p>https://doi.org/10.1088/2057-1976/ad4f73</p>
Drought neutralizes positive effects of long-term grazing on grassland productivity through altering plant-soil interactions
<p>Livestock grazing is among the most intensive land-use activities in grasslands and can affect plant communities directly or indirectly via grazing-induced soil legacies. Under climate change, grasslands are threatened globally by recurrent drought. However, the extent to which drought influences grazing-induced soil legacy effects on plant biomass production and community composition remains largely unexplored.</p> <p>We grew five naturally co-occurring plant species (three dominants and two subordinates) in mixed communities in a glasshouse experiment in live and sterilized soil that had or had not been subjected to 19 years of grazing; these plant communities were then exposed to a subsequent drought. We tested the treatment effects on plant community biomass, proportional aboveground biomass of individual species, arbuscular mycorrhizal (AM) fungal root colonization, and soil nutrient availability.</p> <p>Under drought-free conditions, soils from grazed plots produced significantly higher plant aboveground and total community biomass compared to soils from ungrazed plots. In contrast, plant aboveground and total community biomass were similar between grazed and ungrazed soils under drought conditions. Similarly, soils from grazed plots increased the proportional biomass of dominant species but decreased the proportion of subordinate species; however, the proportional biomass of dominant and subordinate species was similar between grazed and ungrazed soils under drought conditions. Soil NO3--N in grazed soil was significantly higher compared to ungrazed soil. Drought dramatically increased soil NO3--N in sterilized soil and had a more pronounced increase in grazed soil than in ungrazed soil. Arbuscular mycorrhizal fungal root colonization from grazed soil was lower compared to ungrazed soil. Drought significantly increased the soil available phosphorus concentration, as well as plant community AM fungal root colonization.</p> <p>Synthesis. Our study suggests that drought can neutralize positive grazing effects on plant community biomass production via altered plant-soil interactions. Also, we found that drought can alleviate the negative effects of grazing legacies on subordinate species by reducing the competitiveness of dominant species. Our study provides new insights for understanding the underlying mechanisms of grazing effects on grassland productivity under climate change.</p>
RecView: An interactive R application for locating recombination positions using pedigree data
Open the record for dataset details and reuse information.
Drought neutralizes positive effects of long-term grazing on grassland productivity through altering plant-soil interactions
Open the record for dataset details and reuse information.
Positive and negative interspecific interactions between coexisting rice planthoppers neutralize the effects of elevated temperatures
Open the record for dataset details and reuse information.
Enemies with benefits: Integrating positive and negative interactions among terrestrial carnivores
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Metapopulation-level associations in positively interacting stream fishes
Open the record for dataset details and reuse information.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.